Variant report

Variant	rs4928153
Chromosome Location	chr3:99808445-99808446
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:99796671..99799694-chr3:99807406..99810771,4	K562	blood:
2	chr3:99807492..99809231-chr3:99979831..99982167,2	K562	blood:
3	chr3:99808255..99810946-chr3:99815200..99817983,2	MCF-7	breast:
4	chr3:99536338..99538401-chr3:99807558..99809928,2	K562	blood:
5	chr3:99807984..99809965-chr3:99822463..99825380,2	MCF-7	breast:
6	chr3:99806279..99809036-chr3:99909487..99911239,2	K562	blood:
7	chr3:99807438..99810251-chr3:99824386..99825972,2	K562	blood:
8	chr3:99802054..99805861-chr3:99806768..99808957,3	K562	blood:
9	chr3:99796671..99799492-chr3:99807406..99809668,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000036054	Chromatin interaction
ENSG00000184220	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10222474	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10936008	0.80[TSI][hapmap]
rs11711935	0.81[MKK][hapmap]
rs11719468	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs12488245	0.96[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13059754	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap]
rs1387647	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16841874	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs2130369	0.88[CEU][hapmap];0.83[GIH][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs35422475	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4577503	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap]
rs4928150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap]
rs4928151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4928230	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs4928235	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4928237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6767441	0.92[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs6798114	0.84[CEU][hapmap];0.82[AMR][1000 genomes]
rs6802817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6806323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6808765	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs720688	0.81[AMR][1000 genomes]
rs7629487	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7636776	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7638900	0.80[TSI][hapmap]
rs7649349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7650727	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs766778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs793439	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs793440	0.80[TSI][hapmap]
rs793464	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap]
rs796976	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap]
rs902159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs923472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9289981	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9811920	0.83[ASW][hapmap];0.92[CEU][hapmap];0.85[GIH][hapmap];0.96[LWK][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9814549	0.84[CEU][hapmap];0.80[GIH][hapmap];0.82[AMR][1000 genomes]
rs9837131	0.92[CEU][hapmap];0.83[GIH][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9849632	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9865713	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4928153	OR5H6	cis	cerebellum	SCAN
rs4928153	SENP7	cis	parietal	SCAN
rs4928153	EPHX1	trans	cerebellum	SCAN
rs4928153	C3orf26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99793800-99809800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr3:99795800-99866600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99796600-99808800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:99796800-99808600	Weak transcription	Ovary	ovary
5	chr3:99796800-99808800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:99796800-99808800	Weak transcription	Left Ventricle	heart
7	chr3:99798000-99808800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:99800000-99808800	Weak transcription	Aorta	Aorta
9	chr3:99803200-99808800	Weak transcription	Fetal Intestine Small	intestine
10	chr3:99804000-99808800	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr3:99804000-99809000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr3:99804200-99808600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:99804600-99808800	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:99804800-99808600	Weak transcription	Fetal Kidney	kidney
15	chr3:99804800-99808600	Weak transcription	Psoas Muscle	Psoas
16	chr3:99805000-99809600	Enhancers	Muscle Satellite Cultured Cells	--
17	chr3:99806000-99808800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr3:99806000-99808800	Weak transcription	Small Intestine	intestine
19	chr3:99806200-99809800	Enhancers	NHDF-Ad	bronchial
20	chr3:99806200-99816000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:99806200-99818600	Weak transcription	HSMM	muscle
22	chr3:99806600-99808600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:99806600-99808600	Weak transcription	NH-A	brain
24	chr3:99806600-99808600	Weak transcription	NHLF	lung
25	chr3:99806600-99812600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:99806800-99808800	Weak transcription	Fetal Intestine Large	intestine
27	chr3:99806800-99809400	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr3:99806800-99809600	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr3:99806800-99809800	Enhancers	HepG2	liver
30	chr3:99807000-99809800	Enhancers	H1 Cell Line	embryonic stem cell
31	chr3:99807000-99809800	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr3:99807200-99808600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:99807200-99808800	Weak transcription	GM12878-XiMat	blood
34	chr3:99807200-99809600	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr3:99807400-99809200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:99807400-99809200	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr3:99807400-99809400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:99807400-99809400	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr3:99807400-99810600	Enhancers	A549	lung
40	chr3:99807600-99808600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:99807600-99809600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:99807800-99808800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:99807800-99809400	Weak transcription	Liver	Liver
44	chr3:99807800-99810400	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr3:99808000-99809200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
46	chr3:99808000-99809400	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr3:99808000-99809600	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr3:99808000-99809600	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr3:99808400-99808600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:99808400-99809400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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